Cattle are a leading cultivated-meat target, and bovine satellite cells are among the most-studied myogenic systems in the field. This page collects the fixed data artifacts relevant to engineering and modeling bovine cells for cultivated beef: the genome-scale metabolic model, the multi-tissue atlases, and individual transcriptomic / epigenomic deposits spanning satellite-cell heterogeneity, serum-free differentiation, adipogenesis, and breed comparison.
Cattle sub-portal of the FarmGTEx consortium, providing bulk and single-cell multi-tissue expression atlases for cattle (Bos taurus) — directly relevant to cultivated-beef cell-line characterization and engineering. Companion to Papers.md ref #137 (Han et al. 2025, the single-cell atlas paper). Full entry in Databases.md / Livestock Multi-Tissue Atlases.
The FAANG consortium’s cattle functional-annotation project, mapping functionally active genomic features in cattle (Bos taurus); the data hub hosts its open releases. A regulatory-element substrate complementary to CattleGTEx for cultivated-beef cell-line characterisation. Full entry in Databases.md / Livestock Multi-Tissue Atlases.
GEMs are SBML-formatted reconstructions of an organism’s metabolic network — every reaction, every metabolite, every gene-protein-reaction mapping — and are the input data structure for the constraint-based modeling tools listed in Software.md / Metabolic Modeling & Strain Design. The cell-ag GEM ecosystem is fragmented across preprints, supplementary materials, and individual GitHub repos; the bovine reconstruction below inherits network structure from the human reference GEMs catalogued in HumanReference.md.
The first Bos taurus-specific genome-scale metabolic model (GEM), built for cultured-meat research and published 2024 by Lee et al. as a bioRxiv preprint. The model integrates multi-omics data, was reconstructed on the human1 GEM as a template, and contains ~13,278 reactions across 2,986 genes, with biomass functions parameterized for cultivated-meat-relevant bovine cell types. Designed to support FBA-driven identification of media supplement combinations and metabolic bottlenecks for cultivated beef production. SBML files are distributed via the preprint’s supplementary materials.
Reference: Papers.md #81 (Lee et al. 2024, bioRxiv).
The most directly cultivated-meat-relevant bovine datasets profile satellite cells — the myogenic progenitors cultivated beef is grown from — across isolation, expansion, and differentiation. Single-cell RNA-seq of cultured bovine satellite cells (GSE184128) and of muscle-derived cell types sampled across long-term culture (GSE211428) characterise the heterogeneity and drift of the starting population, while single-nucleus RNA-seq of serum-free differentiation (GSE240556) and the serum-free media-formulation study (GSE173199) map the transcriptional response to the FBS-replacement strategies central to scaling cultivated beef. The Tufts/Kaplan lab’s Stout et al. 2022 (Communications Biology) — the foundational reference for these SFM transcriptomic studies — adapts the B8 pluripotent-stem-cell serum-free medium for sustained bovine satellite cell expansion across multiple passages without serum or growth-factor-rich supplements, establishing the SFM benchmark cultivated-beef labs build on. An enhanced-media multi-omics study from the Bar-Nur lab (Trautmann et al. 2025, Advanced Science) profiles bovine myoblast lines from four muscles under small-molecule cocktails (forskolin + RepSox ± CHIR99021) versus conventional differentiation media in both 2D and tissue-engineered 3D models, with paired bulk RNA-seq, scRNA-seq, and LC-MS proteomics (GSE262758 + PRIDE PXD051019). A CRISPR/Cas9 cell-line-engineering deposit extends the cluster beyond media and differentiation into allergen removal: D’Costa et al. 2026 (bioRxiv) disrupt GGTA1 (α1,3-galactosyltransferase) in immortalized bovine satellite cells to eliminate the galactose-α-1,3-galactose (alpha-gal) epitope responsible for Alpha-gal Syndrome, with bulk RNA-seq of three control and three knockout clones before and after differentiation confirming minimal global transcriptional disruption and preserved myogenic capacity (GSE330550).
A second cluster maps the regulatory genome of bovine skeletal muscle. Single-cell RNA-seq plus scATAC-seq of developing muscle (CRA006626) and ATAC-seq across indicine cattle tissues (GSE182909) resolve the chromatin landscape underlying myogenic development, and the multi-species functional-annotation effort (GSE158430, which also covers pig — see Pig.md) adds CTCF ChIP-seq and ATAC-seq across eight tissues. A companion bovine myoblast proliferation/differentiation dataset is listed in the inventory for completeness though its SRA accession is marked unavailable in the source survey. Whole-genome bisulfite sequencing paired with transcriptome sequencing of bovine satellite cells under sodium butyrate (Wang et al. 2024, Genomics, PRJNA1056565) extends the cluster into methylome-level regulation of differentiation, directly relevant to chromatin-modulator-driven cultivated-beef process design.
Marbling — intramuscular fat — is a key cultivated-beef quality target. A single-cell atlas of bovine skeletal muscle (GSE205347) dissects the adipogenic and fibrogenic cell populations across Wagyu, Brahman, and crossbred calves, complemented by a Wagyu-vs-Chinese-Red-Steppe differential-expression study (GSE161967) and a Hanwoo satellite-cell differentiation dataset spanning two muscle groups. Three further studies extend the cluster: a satellite-cell-derived-exosome study showing modulation of preadipocyte adipogenesis via bta-miR-2904 (Sun et al. 2026, Animals, CNCB PRJCA054990), a miR-10167-3p / TCF7L1 regulatory study in bovine preadipocytes (Hu et al. 2024, Genomics), and an integrated multi-omics meat-quality comparison of Liangshan vs Simmental crossbred cattle longissimus dorsi (Wang et al. 2025, Food Chemistry: Molecular Sciences) that ties l-carnitine, energy-metabolism, and fatty-acid-composition differences to breed-specific regulation.
Beyond the cultured-cell deposits above, a cluster of conventional-beef postmortem omics studies maps the muscle-to-meat conversion that cultivated beef must ultimately reproduce in colour, texture, and flavour. Tandem-mass-tag proteomics of early-postmortem longissimus lumborum and psoas major (Zhai et al. 2020, Journal of Proteomics, PRIDE PXD017535) resolves muscle-specific proteome divergence across the first 36 h postmortem; two dark-cutting-beef studies from Kiyimba et al. (2021, 2022, Journal of Proteomics) profile the glycolytic, mitochondrial-biogenesis, and bioenergetic protein signatures behind the high-ultimate-pH “dark, firm, dry” defect; and a postmortem-aging study (Yang et al. 2021, PLOS ONE) ties differentially abundant proteins to beef quality across the aging window. These conventional-meat-quality proteomes are reference substrate for the sensory- and quality-prediction models cultivated beef is benchmarked against (see Sensory Prediction). The cluster also gathers beef meat-quality metabolomics — NMR profiling of dark-cutting longissimus (Cônsolo et al. 2021) and of meat-exudate aging (Castejón et al. 2015), and HPLC-MS profiling of postmortem colour/lipid stability across muscles (Ma et al. 2017) — a label-free plasma/muscle proteome of sensory tenderness, juiciness, and chewiness biomarkers (Zhu et al. 2021), and a cross-species LC-MS/MS reference (Zhang et al. 2022) whose validated MRM marker peptides discriminate seven meat species including cattle. Only Zhai et al. deposited raw spectra to a repository (PRIDE); every other entry in this cluster released its data as open supplementary tables (noted per row).
Distinct from the omics deposits above, computer-vision datasets capture the visible surface cues — colour, texture, and surface condition — that inspectors and consumers read as freshness, and that cultivated beef must ultimately reproduce. MeatScan (Gyening et al. 2025, Data in Brief; companion to Papers.md #196) is an 11,000-image RGB collection (5,627 fresh / 5,373 spoiled) of cow meat photographed in real-world Ghanaian open-air markets, butcher shops, and cold-storage facilities, each image labelled fresh-vs-spoiled under natural lighting by trained collectors. It is training data for the MobileNet-class freshness classifiers that meat-quality and Sensory Prediction models are benchmarked on — and a deliberately low-resource, real-world-conditions counterpoint to the lab-controlled spectroscopy and hyperspectral approaches.
A curated snapshot. NCBI accessions are the canonical living source — fetch the linked accession for current sample counts, file sizes, and availability.
| Study | Paper | Data | Type | Tissue | Description | Size | Area of research |
|---|---|---|---|---|---|---|---|
| Single-cell RNA sequencing reveals heterogeneity of cultured bovine satellite cells | DOI | GSE184128 | scRNA-seq | Muscle | Satellite cells from a male calf, one week in growth medium, two 10x libraries | 265.1 Gb, 860 M reads | Satellite-cell heterogeneity |
| Single-cell analysis of bovine muscle-derived cell types for cultured meat production | DOI | GSE211428 | scRNA-seq | Muscle | 5 time points across long-term culture: post-isolation, 72 h, passages 2/5/8 | 462.12 Gb | Cultured meat |
| Optimisation of cell fate determination for cultured muscle differentiation | DOI | GSE240556 | snRNA-seq | Muscle | Bovine satellite cells in serum-free differentiation medium, harvested 0/24/48/72/96 h | 52.97 Gb | Cultured meat |
| A serum-free media formulation for cultured meat production supports bovine satellite cell differentiation | DOI | GSE173199 | RNA-seq | Muscle | Serum-starvation series (20%→2% FBS) and SFM vs 20% FBS comparison | 93.25 Gb | Cultured meat |
| Simple and effective serum-free medium for sustained expansion of bovine satellite cells for cell cultured meat | DOI | on request | SFM development + functional assays | Muscle (satellite cells) | B8 pluripotent-stem-cell serum-free medium adapted for sustained bovine satellite cell expansion across multiple passages (Tufts/Kaplan lab; Stout, Mirliani, Rittenberg, Shub, White, Yuen & Kaplan 2022, Communications Biology); no public repository accession — data in paper’s Supplementary files + corresponding author on request | — | Cell-ag-direct SFM development |
| CRISPR-mediated engineering of bovine satellite cells for AGS-compatible cultivated meat | preprint | GSE330550 | bulk RNA-seq | Muscle (immortalized satellite cells) | Three control and three GGTA1-knockout iBSC clones profiled before and after differentiation; CRISPR/Cas9 homozygous frameshift disruption of GGTA1 (α1,3-galactosyltransferase) eliminates the alpha-gal epitope while preserving myogenic identity and differentiation capacity, toward Alpha-gal Syndrome–compatible cultivated beef (D’Costa et al. 2026, bioRxiv) | — | Cell-line engineering (allergen removal) |
| Transcriptional and open chromatin analysis of bovine skeletal muscle development by single-cell sequencing | DOI | CRA006626 | scRNA-seq + scATAC-seq | Muscle | Developing bovine skeletal muscle across gestational, lactational, and adult stages | — | Developmental biology |
| Functional annotations of three domestic animal genomes | DOI | GSE158430 | ChIP-seq + ATAC-seq | 8 tissues incl. skeletal muscle, adipose | ATAC-seq and CTCF ChIP-seq across 8 tissues; one multi-species GEO deposit, also covers pig (see Pig.md) | 6.8 B ChIP-seq + 1.19 B ATAC-seq reads (cattle-relevant figure from the source survey) | Comparative epigenomics |
| Transcriptional states and chromatin accessibility during bovine myoblast proliferation and differentiation | DOI | PRJNA790762 | RNA-seq + ATAC-seq | Muscle | Chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) across bovine myoblast proliferation and myogenic differentiation | 33 SRA runs | Epigenetics, developmental biology |
| Chromatin accessibility and regulatory vocabulary across indicine cattle tissues | DOI | GSE182909 | ATAC-seq + RNA-seq | Liver, Muscle, Hypothalamus | ATAC-seq in liver, muscle, hypothalamus of indicine cattle (also GEO GSB-113, GSB-8708) | 60.74 Gb | Epigenetics, developmental biology |
| A single-cell atlas of bovine skeletal muscle reveals mechanisms regulating intramuscular adipogenesis and fibrogenesis | DOI | GSE205347 | scRNA-seq | Muscle | Longissimus dorsi cells from 4-month Wagyu, Brahman, and crossbred heifer calves | 765.33 Gb | Adipogenesis & fibrogenesis |
| RNA-Seq analysis identifies differentially expressed genes in the longissimus dorsi of Wagyu and Chinese Red Steppe cattle | DOI | GSE161967 | RNA-seq | Muscle | Wagyu and Chinese Red Steppe cattle slaughtered at 28 months, longissimus dorsi, triplicate | 26.85 Gb | Breed comparison & meat quality |
| Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus | DOI | on request | RNA-seq | Muscle | LD and SM muscle of three Korean Hanwoo newborn calves; RNA-seq data available on request | ~35.7 M reads/sample | Embryonic myogenesis |
| Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications | DOI | GSE262758 | RNA-seq + scRNA-seq + LC-MS proteomics | Muscle | Bovine myoblast lines from four muscles (MA, MM, PM, MLL) differentiated under iFRhi or iFRC small-molecule cocktails (forskolin + RepSox ± CHIR99021) vs conventional differentiation media, in 2D and tissue-engineered 3D models; proteomics also at PRIDE PXD051019; 11k–19k cells per scRNA-seq dataset | — | Cultivated-meat media development |
| Bovine Muscle Satellite Cell-Derived Exosomes Modulate Preadipocyte Adipogenesis via bta-miR-2904 | DOI | PRJCA054990 | microRNA-seq | Muscle, Fat | Exosomes isolated from bovine muscle satellite cells; bta-miR-2904 identified as a regulator of preadipocyte adipogenesis | — | Adipogenesis regulation |
| miR-10167-3p targets TCF7L1 to inhibit bovine adipocyte differentiation and promote bovine adipocyte proliferation | DOI | on request | RNA-seq + miRNA functional assays | Fat (preadipocytes) | Bovine preadipocytes; miR-10167-3p / TCF7L1 regulatory axis controlling preadipocyte proliferation vs differentiation; no public deposit (data available on request per the paper) | — | Adipogenesis regulation |
| Integrative analysis of whole genome bisulfite and transcriptome sequencing reveals the effect of sodium butyrate on DNA methylation in the differentiation of bovine skeletal muscle satellite cells | DOI | PRJNA1056565 | RNA-seq + whole-genome bisulfite sequencing | Muscle | Bovine skeletal muscle satellite cells ± sodium butyrate | — | Epigenetics & differentiation |
| Integrated multi-omics reveals potential regulatory mechanisms of meat quality | DOI | on request | RNA-seq + untargeted metabolomics + GC–MS fatty acids + targeted amino acids | Muscle (longissimus dorsi) | Liangshan cattle vs Simmental crossbred cattle; identifies l-carnitine upregulation and FASN/ALDOC/PFKL/PGAM1/SDS as breed-distinguishing energy-metabolism markers; no public deposit (data available on request per the paper) | — | Breed comparison & meat quality |
| Tandem mass tag labeling to characterize muscle-specific proteome changes in beef during early postmortem period | DOI | PXD017535 | TMT LC-MS/MS proteomics | Muscle (longissimus lumborum + psoas major) | Early-postmortem proteome of two beef muscles sampled at 45 min, 12 h, and 36 h from four carcasses (Zhai et al. 2020, Journal of Proteomics); companion Data in Brief 10.1016/j.dib.2020.106064 | 4 carcasses × 2 muscles × 3 timepoints | Postmortem proteome & meat quality |
| Changes in glycolytic and mitochondrial protein profiles regulates postmortem muscle acidification and oxygen consumption in dark-cutting beef | DOI | supplementary | LC-MS/MS proteomics | Muscle | Dark-cutting vs normal-pH beef glycolytic/mitochondrial proteome (Kiyimba et al. 2021, Journal of Proteomics); full MaxQuant protein-groups quantification released as open supplementary data (mmc2.xlsx) — supplementary data, not a repository deposit | — | Postmortem proteome & meat quality |
| Dark-cutting beef mitochondrial proteomic signatures reveal increased biogenesis proteins and bioenergetics capabilities | DOI | supplementary | LC-MS/MS proteomics (mitochondrial) | Muscle | Mitochondrial proteome of dark-cutting vs normal-pH beef (Kiyimba et al. 2022, Journal of Proteomics); complete dataset released as open supplementary data (mmc1.xlsx) — supplementary data, not a repository deposit | — | Postmortem proteome & meat quality |
| Application of proteomics to understand the molecular mechanisms determining meat quality of beef muscles during postmortem aging | DOI | supplementary | LC-MS/MS proteomics | Muscle | Beef postmortem-aging time-course (Yang et al. 2021, PLOS ONE); differentially expressed proteins with per-sample abundances plus GO/KEGG enrichment released as open Supporting Information (S1 Table) — supplementary data, not a repository deposit | — | Postmortem proteome & meat quality |
| Shotgun proteomics for the preliminary identification of biomarkers of beef sensory tenderness, juiciness and chewiness from plasma and muscle of young Limousin-sired bulls | DOI | supplementary | Label-free LC-MS/MS proteomics | Plasma + muscle | Young Limousin-sired bulls; candidate plasma and muscle protein biomarkers of sensory tenderness, juiciness, and chewiness (Zhu et al. 2021, Meat Science); protein identification/quantification and correlation tables in open Supporting Information (Appendix A) — supplementary data, not a repository deposit | — | Sensory-trait proteomics |
| Preliminary study on the characterization of Longissimus lumborum dark cutting meat in Angus × Nellore crossbreed cattle using NMR-based metabolomics | DOI | supplementary | ¹H-NMR metabolomics | Muscle (longissimus lumborum) | Dark-cutting vs normal-pH longissimus in Angus × Nellore cattle (Cônsolo et al. 2021, Meat Science); descriptive statistics for the 45 quantified ¹H-NMR metabolites in Supplemental Table S1 (metabolite concentrations in main-text Table 2, PLS-DA VIP scores in Fig. 2b) — supplementary data, not a repository deposit | — | Dark-cutting metabolomics |
| Metabolomics of meat exudate: its potential to evaluate beef meat conservation and aging | DOI | supplementary | ¹H / 2D-NMR metabolomics | Muscle exudate | Beef meat-exudate NMR metabolomics across conservation and aging (Castejón et al. 2015, Analytica Chimica Acta); the 54-bucket NMR feature-definition table (the 48×54 PCA/PLS input matrix) plus 2D-NMR metabolite assignments in Supplementary Data — supplementary data, not a repository deposit | — | Meat-aging metabolomics |
| Metabolomics profiling to determine the effect of postmortem aging on color and lipid oxidative stabilities of different bovine muscles | DOI | supplementary | HPLC-MS metabolomics | Muscle (multiple) | Postmortem-aging colour and lipid-oxidation metabolomics across bovine muscles (Ma et al. 2017, J. Agric. Food Chem.); principal-component loadings and metabolite–trait correlation matrices in ACS Supporting Information — supplementary data, not a repository deposit | — | Postmortem metabolome & meat quality |
| Rapid LC-MS/MS method for the detection of seven animal species in meat products | DOI | supplementary | LC-MS/MS (targeted MRM marker peptides) | Muscle (seven meat species) | Validated species-specific marker peptides discriminating seven meat species — pig, cattle, sheep, deer, chicken, duck, and turkey (Zhang et al. 2022, Food Chemistry); the marker-peptide MRM transition table (parent and product ion m/z, retention time, collision energy per marker) and per-species protein concentrations in Supplementary Tables 1–2 (marker peptides also tabulated in main-text Table 2) — supplementary data, not a repository deposit | — | Meat-species authentication |
| MeatScan: an image dataset for fresh/spoiled cow-meat classification | DOI | Zenodo | RGB image dataset (computer vision) | Muscle (whole cuts) | 11,000 high-resolution RGB images (5,627 fresh, 5,373 spoiled) of cow meat photographed in Ghanaian markets, butcher shops, and cold storage, labelled for fresh-vs-spoiled binary classification (Gyening et al. 2025, Data in Brief; companion to Papers.md #196) | 11,000 images | Meat-quality imaging |
| Electronic nose dataset for beef quality monitoring in uncontrolled ambient conditions | DOI | Mendeley | E-nose gas-sensor time-series | Muscle (beef) | Metal-oxide gas-sensor array recordings of beef spoilage under uncontrolled ambient conditions; five time-series CSV files (TS1–TS5) pairing sensor resistances with microbial total-viable-count and 1–4 quality labels (Wijaya, Sarno & Zulaika 2018, Data in Brief; Mendeley v3) | 5 CSV time-series | Meat-quality e-nose sensing |
| Electronic nose homogeneous data sets for beef quality classification and microbial population prediction | DOI | Dataverse | E-nose gas-sensor time-series | Muscle (12 beef cuts) | 11 metal-oxide gas sensors tracking spoilage across 12 beef cuts (round, sirloin, tenderloin, brisket, rib eye, and others) over 2220 min; one xlsx sheet per cut with sensor resistances, continuous total-viable-count, and four-level quality labels (Wijaya, Sarno, Zulaika & Afianti 2022, BMC Research Notes) | 12 cuts × 2220 min | Meat-quality e-nose sensing |
| Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells | DOI | GSE179821 | ChIP-seq (histone marks) | Muscle (satellite cells) | Histone-mark ChIP-seq of bovine satellite cells before and 2 days after induced differentiation (two cattle, two states) mapping active enhancers and transcription-factor programs of myogenic differentiation (Lyu, Settlage & Jiang 2021, BMC Genomics) | 6 ChIP-seq libraries | Enhancer/TF regulation of myogenesis |
| Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation | DOI | GSE253395 | ChIP-seq (H3K4me1, H3K27ac, H3K27me3) | Muscle (satellite cells) | Histone-mark ChIP-seq of proliferating vs differentiating bovine satellite cells (two cattle) identifying TFAP4 as a critical transcriptional regulator of differentiation, validated by knockdown and overexpression (Lyu & Jiang 2024, BMC Genomics) | 16 sequencing libraries | TF regulation of differentiation |
| An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome | preprint | unavailable | ATAC-seq + ChIP-seq + WGBS + Hi-C + RNA-seq | 53 adult + 5 fetal tissues + 7 primary cell types | Bovine FAANG epigenome atlas of 1,147 genome-wide profiles (158 RNA-seq, 204 ATAC-seq, 91 WGBS, 682 histone/CTCF ChIP-seq, 12 Hi-C) annotating ~45% of the genome as putative regulatory elements; newly generated deposits embargoed until journal acceptance (reused public data PRJEB41939, PRJNA672996, PRJNA531208, E-MTAB-11825/11826; pipelines at github.com/guandailu/BovineFAANG) (Guan et al. 2025, bioRxiv) | 1,147 profiles | Regulatory-element annotation |
| Synergetic hallmark knockouts immortalize bovine muscle stem cells for cellular agriculture | preprint | on request | bulk RNA-seq | Muscle (satellite cells; CriBSC lines) | CRISPR/Cas9 knockout of PTEN, TP53, and SMAD4 immortalizes bovine satellite cells into the CriBSC2 line, which keeps myogenic identity and forms myotubes past 150 divisions and on gelatin scaffolds; RNA-seq contrasts immortalized and primary cells (Tufts/Kaplan lab; Zhang, Bromberg, Gordon, Nagarajan, Stout, Hasturk, Sim, Brennan, La, Fernandez, David, White & Kaplan 2025, bioRxiv); GEO accession available on request per the data-availability statement | — | Cell-line engineering (immortalization) |
Curation source: The cultured-cell and developmental deposits above were initially curated from the supplemental Table 1 of Todhunter et al. 2024 (Papers.md ref #132); subsequent additions come from CAAIL contributors. The postmortem proteome & meat-quality entries were curated by walking the cited references of the Encyclopedia of Meat Sciences (2024) reviews on proteomics (Gagaoua et al. 2024) and metabolomics (Kiyimba et al. 2024) in meat research.
Databases.md. Foundational reference for the CattleGTEx lineage: Papers.md #192 (Liu et al. 2022, Nature Genetics).Software.md.Linked external resources are independent of TUCCA and Tufts University and remain under their own licenses.